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| # Copyright 2021 DeepMind Technologies Limited | |
| # | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| """Library to run HHblits from Python.""" | |
| import glob | |
| import os | |
| import subprocess | |
| from typing import Any, Mapping, Optional, Sequence | |
| from absl import logging | |
| from alphafold.data.tools import utils | |
| # Internal import (7716). | |
| _HHBLITS_DEFAULT_P = 20 | |
| _HHBLITS_DEFAULT_Z = 500 | |
| class HHBlits: | |
| """Python wrapper of the HHblits binary.""" | |
| def __init__(self, | |
| *, | |
| binary_path: str, | |
| databases: Sequence[str], | |
| n_cpu: int = 4, | |
| n_iter: int = 3, | |
| e_value: float = 0.001, | |
| maxseq: int = 1_000_000, | |
| realign_max: int = 100_000, | |
| maxfilt: int = 100_000, | |
| min_prefilter_hits: int = 1000, | |
| all_seqs: bool = False, | |
| alt: Optional[int] = None, | |
| p: int = _HHBLITS_DEFAULT_P, | |
| z: int = _HHBLITS_DEFAULT_Z): | |
| """Initializes the Python HHblits wrapper. | |
| Args: | |
| binary_path: The path to the HHblits executable. | |
| databases: A sequence of HHblits database paths. This should be the | |
| common prefix for the database files (i.e. up to but not including | |
| _hhm.ffindex etc.) | |
| n_cpu: The number of CPUs to give HHblits. | |
| n_iter: The number of HHblits iterations. | |
| e_value: The E-value, see HHblits docs for more details. | |
| maxseq: The maximum number of rows in an input alignment. Note that this | |
| parameter is only supported in HHBlits version 3.1 and higher. | |
| realign_max: Max number of HMM-HMM hits to realign. HHblits default: 500. | |
| maxfilt: Max number of hits allowed to pass the 2nd prefilter. | |
| HHblits default: 20000. | |
| min_prefilter_hits: Min number of hits to pass prefilter. | |
| HHblits default: 100. | |
| all_seqs: Return all sequences in the MSA / Do not filter the result MSA. | |
| HHblits default: False. | |
| alt: Show up to this many alternative alignments. | |
| p: Minimum Prob for a hit to be included in the output hhr file. | |
| HHblits default: 20. | |
| z: Hard cap on number of hits reported in the hhr file. | |
| HHblits default: 500. NB: The relevant HHblits flag is -Z not -z. | |
| Raises: | |
| RuntimeError: If HHblits binary not found within the path. | |
| """ | |
| self.binary_path = binary_path | |
| self.databases = databases | |
| for database_path in self.databases: | |
| if not glob.glob(database_path + '_*'): | |
| logging.error('Could not find HHBlits database %s', database_path) | |
| raise ValueError(f'Could not find HHBlits database {database_path}') | |
| self.n_cpu = n_cpu | |
| self.n_iter = n_iter | |
| self.e_value = e_value | |
| self.maxseq = maxseq | |
| self.realign_max = realign_max | |
| self.maxfilt = maxfilt | |
| self.min_prefilter_hits = min_prefilter_hits | |
| self.all_seqs = all_seqs | |
| self.alt = alt | |
| self.p = p | |
| self.z = z | |
| def query(self, input_fasta_path: str) -> Mapping[str, Any]: | |
| """Queries the database using HHblits.""" | |
| with utils.tmpdir_manager(base_dir='/tmp') as query_tmp_dir: | |
| a3m_path = os.path.join(query_tmp_dir, 'output.a3m') | |
| db_cmd = [] | |
| for db_path in self.databases: | |
| db_cmd.append('-d') | |
| db_cmd.append(db_path) | |
| cmd = [ | |
| self.binary_path, | |
| '-i', input_fasta_path, | |
| '-cpu', str(self.n_cpu), | |
| '-oa3m', a3m_path, | |
| '-o', '/dev/null', | |
| '-n', str(self.n_iter), | |
| '-e', str(self.e_value), | |
| '-maxseq', str(self.maxseq), | |
| '-realign_max', str(self.realign_max), | |
| '-maxfilt', str(self.maxfilt), | |
| '-min_prefilter_hits', str(self.min_prefilter_hits)] | |
| if self.all_seqs: | |
| cmd += ['-all'] | |
| if self.alt: | |
| cmd += ['-alt', str(self.alt)] | |
| if self.p != _HHBLITS_DEFAULT_P: | |
| cmd += ['-p', str(self.p)] | |
| if self.z != _HHBLITS_DEFAULT_Z: | |
| cmd += ['-Z', str(self.z)] | |
| cmd += db_cmd | |
| logging.info('Launching subprocess "%s"', ' '.join(cmd)) | |
| process = subprocess.Popen( | |
| cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) | |
| with utils.timing('HHblits query'): | |
| stdout, stderr = process.communicate() | |
| retcode = process.wait() | |
| if retcode: | |
| # Logs have a 15k character limit, so log HHblits error line by line. | |
| logging.error('HHblits failed. HHblits stderr begin:') | |
| for error_line in stderr.decode('utf-8').splitlines(): | |
| if error_line.strip(): | |
| logging.error(error_line.strip()) | |
| logging.error('HHblits stderr end') | |
| raise RuntimeError('HHblits failed\nstdout:\n%s\n\nstderr:\n%s\n' % ( | |
| stdout.decode('utf-8'), stderr[:500_000].decode('utf-8'))) | |
| with open(a3m_path) as f: | |
| a3m = f.read() | |
| raw_output = dict( | |
| a3m=a3m, | |
| output=stdout, | |
| stderr=stderr, | |
| n_iter=self.n_iter, | |
| e_value=self.e_value) | |
| return raw_output | |